references.bib

@article{Ying:2004:JCP,
    author        = {Lexing Ying, George Biros, Denis Zorin},
    title         = {A kernel-independent adaptive fast multipole algorithm in two and three dimensions},
    journaltitle  = {Journal of Computational Physics},
    year          = {2004},
    volume        = {196},
    number        = {2},
    pages         = {591-626},
    doi           = {http://dx.doi.org/10.1016/j.jcp.2003.11.021}
}

@online{exafmm,
    author        = {Rio Yokota, Lorena A. Barba},
    title         = {ExaFMM User's Manual},
    year          = {2011},
    url           = {http://www.bu.edu/exafmm/files/2011/06/ExaFMM-UserManual1.pdf}
}

@book{latexcompanion,
    author        = {Michel Goossens and Frank Mittelbach and Alexander Samarin},
    title         = {The \LaTeX\ Companion},
    year          = {1993},
    publisher     = {Addison-Wesley},
    location      = {Reading, Massachusetts}
}

@phdthesis{Greengard:1987:Yale,
  author      = {Leslie Greengard},
  title       = {The Rapid Evaluation of Potential Fields in Particle Systems},
  school      = {Yale University},
  year        = {1987}
}

@article{Cipra:2000:SN,
  author          = {Barry A. Cipra},
  title           = {The Best of the 20th Century: Editors Name Top 10 Algorithms},
  journal         = {SIAM News},
  volume          = {33},
  number          = {4},
  year            = {2000}
}

@conference{Beatson:1997:SCF,
  author          = {Rick Beatson and Leslie Greengard},
  title           = {A Short Course on Fast Multipole Methods},
  booktitle       = {Wavelets, Multilevel Methods, and Elliptic PDEs},
  publisher       = {Clarendon Press},
  year            = {1997}
}

@book{Griffiths:2017:CUP,
    place={Cambridge},
    edition={4},
    title={Introduction to Electrodynamics},
    DOI={10.1017/9781108333511},
    publisher={Cambridge University Press},
    author={Griffiths, David J.},
    year={2017}
}

@article{Rokhlin:1990:JCP,
       author = {Vladimir Rokhlin},
        title = "{Rapid Solution of Integral Equations of  Theory in Two Dimensions}",
      journal = {Journal of Computational Physics},
         year = 1990,
        month = feb,
       volume = {86},
       number = {2},
        pages = {414-439},
          doi = {10.1016/0021-9991(90)90107-C},
}

@article{Board:1992:CPL,
          author = "John A. Board and Jeffrey W. Causey and James F. Leathrum and Andreas Windemuth and Klaus Schulten",
          title = "Accelerated molecular dynamics simulation with the parallel fast multipole algorithm",
          journal = "Chemical Physics Letters",
          volume = "198",
          number = "1",
          pages = "89 - 94",
          year = 1992,
          issn = "0009-2614",
          doi = "https://doi.org/10.1016/0009-2614(92)90053-P",
          url = "http://www.sciencedirect.com/science/article/pii/000926149290053P",
}

@book{Hwu:2011:MKP,
author = {Wen-Mei W. Hwu},
title = {GPU Computing Gems Emerald Edition},
year = {2011},
isbn = {0123849888},
publisher = {Morgan Kaufmann Publishers Inc.},
address = {San Francisco, CA, USA},
edition = {1st}
}

@article{Etheridge:2001:SIAM,
author = {Frank Ethridge and Leslie Greengard},
title = {A New Fast-Multipole Accelerated Poisson Solver in Two Dimensions},
year = {2001},
issue_date = {2001},
publisher = {Society for Industrial and Applied Mathematics},
address = {USA},
volume = {23},
number = {3},
issn = {1064-8275},
url = {https://doi.org/10.1137/S1064827500369967},
doi = {10.1137/S1064827500369967},
abstract = {We present an adaptive fast multipole method for solving the Poisson equation in two dimensions. The algorithm is direct, assumes that the source distribution is discretized using an adaptive quad-tree, and allows for Dirichlet, Neumann, periodic, and free-space conditions to be imposed on the boundary of a square. The amount of work per grid point is comparable to that of classical fast solvers, even for highly nonuniform grids.},
journal = {SIAM J. Sci. Comput.},
month = mar,
pages = {741–760},
numpages = {20},
keywords = {adaptive refinement, fast Poisson solver, fast multipole method, Poisson equation}
}

@article{Greengard:1996:JCP,
title = "A direct adaptive poisson solver of arbitrary order accuracy",
abstract = "We present a direct, adaptive solver for the Poisson equation which can achieve any prescribed order of accuracy. It is based on a domain decomposition approach using local spectral approximation, as well as potential theory and the fast multipole method. In two space dimensions, the algorithm requires O(NK) work, where N is the number of discretization points and K is the desired order of accuracy.",
author = "Leslie Greengard and Lee, {June Yub}",
year = "1996",
month = may,
doi = "10.1006/jcph.1996.0103",
language = "English (US)",
volume = "125",
pages = "415--424",
journal = "Journal of Computational Physics",
issn = "0021-9991",
publisher = "Academic Press Inc.",
number = "2",
}

@book{Trefethen:1997:SIAM,
  added-at = {2010-09-19T02:35:23.000+0200},
  author = {Trefethen, Lloyd N. and Bau, David},
  biburl = {https://www.bibsonomy.org/bibtex/2e45a2ed5ccc6dc12721cde613217c222/ytyoun},
  interhash = {1e7e7a44cbff3092be50a71fe056c8ec},
  intrahash = {e45a2ed5ccc6dc12721cde613217c222},
  isbn = {0898713617},
  keywords = {characteristic eigenvalues linear.algebra matrix numerical numerical.analysis polynomial secular.equation textbook},
  publisher = {SIAM},
  timestamp = {2017-11-25T07:18:16.000+0100},
  title = {Numerical Linear Algebra},
  year = 1997
}

@article{Malhotra:2015:CCP,
 title={PVFMM: A Parallel Kernel Independent FMM for Particle and Volume Potentials},
 volume={18},
 DOI={10.4208/cicp.020215.150515sw},
 number={3},
 journal={Communications in Computational Physics},
 publisher={Cambridge University Press},
 author={Malhotra, Dhairya and Biros, George},
 year={2015}, pages={808–830}
 }

@article{Barnett:2008:JCP,
author = {Barnett, A. H. and Betcke, T.},
title = {Stability and Convergence of the Method of Fundamental Solutions for Helmholtz Problems on Analytic Domains},
year = {2008},
issue_date = {July, 2008},
publisher = {Academic Press Professional, Inc.},
address = {USA},
volume = {227},
number = {14},
issn = {0021-9991},
url = {https://doi.org/10.1016/j.jcp.2008.04.008},
doi = {10.1016/j.jcp.2008.04.008},
abstract = {The method of fundamental solutions (MFS) is a popular tool to solve Laplace and Helmholtz boundary value problems. Its main drawback is that it often leads to ill-conditioned systems of equations. In this paper, we investigate for the interior Helmholtz problem on analytic domains how the singularities (charge points) of the MFS basis functions have to be chosen such that approximate solutions can be represented by the MFS basis in a numerically stable way. For Helmholtz problems on the unit disc we give a full analysis which includes the high frequency (short wavelength) limit. For more difficult and nonconvex domains such as crescents we demonstrate how the right choice of charge points is connected to how far into the complex plane the solution of the boundary value problem can be analytically continued, which in turn depends on both domain shape and boundary data. Using this we develop a recipe for locating charge points which allows us to reach error norms of typically 10^-^1^1 on a wide variety of analytic domains. At high frequencies of order only 3 points per wavelength are needed, which compares very favorably to boundary integral methods.},
journal = {J. Comput. Phys.},
month = jul,
pages = {7003–7026},
numpages = {24},
keywords = {Analytic continuation, 65N35, Method of fundamental solutions, High frequency waves, Boundary value problem, 65N12, Helmholtz equation, 78M25}
}

@article{Sundar:2008:SIAM,
  title={Bottom-up construction and 2: 1 balance refinement of linear octrees in parallel},
  author={Sundar, Hari and Sampath, Rahul S and Biros, George},
  journal={SIAM Journal on Scientific Computing},
  volume={30},
  number={5},
  pages={2675--2708},
  year={2008},
  publisher={SIAM}
}

@TechReport{Campbell:2003:Williams,
  author = 	 {Paul M. Campbell and Karen D. Devine and Joseph E. Flaherty and Luis G. Gervasio and James D. Teresco},
  title = 	 {Dynamic Octree Load Balancing Using Space-Filling Curves},
  institution =  {Williams College Department of Computer Science},
  year = 	 {2003},
  number = 	 {CS-03-01}
}

@Blog{Wasser:NSF,
title={Hierarchical Data Formats - What is HDF5?},
url={https://www.neonscience.org/about-hdf5},
journal={NSF NEON | Open Data to Understand our Ecosystems},
publisher={National Science Foundation},
author={Leah A. Wasser}
}

@book{Ramalho:2015:Oreilly,
author = {Luciano Ramalho},
title = {Fluent Python},
year = {2015},
isbn = {1491946008},
publisher = {O'Reilly Media, Inc.},
edition = {1st},
}

@article{Halko:2011:SIAM,
author = {Nathan Halko, Per-Gunnar Martinsson and Joel Tropp},
year = {2011},
month = {01},
pages = {217-288},
title = {Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions},
volume = {53},
journal = {SIAM Review},
doi = {10.1137/090771806}
}

@website{mahout,
title={Apache Mahout - Distributed Linear Algebra},
url={https://mahout.apache.org/},
}

@article{Erichson:2019:JOSS,
author = {Erichson, N. Benjamin and Voronin, Sergey and Brunton, Steven and Kutz, J.},
year = {2019},
month = {06},
pages = {},
title = {Randomized Matrix Decompositions Using R},
volume = {89},
journal = {Journal of Statistical Software},
doi = {10.18637/jss.v089.i11}
}

@book{Gamma:1994:Addison,
  asin = {0201633612},
  author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John M.},
  edition = 1,
  isbn = {0201633612},
  publisher = {Addison-Wesley Professional},
  title = {Design Patterns: Elements of Reusable Object-Oriented Software},
  year = 1994
}

@book{hughes2010measurements,
  title={Measurements and Their Uncertainties: A Practical Guide to Modern Error Analysis},
  author={Hughes, I. and Hase, T.},
  isbn={9780199566327},
  lccn={2010281028},
  url={https://books.google.co.uk/books?id=AbEVDAAAQBAJ},
  year={2010},
  publisher={OUP Oxford}
}

@book{collette2013python,
  title={Python and HDF5},
  author={Collette, A.},
  isbn={9781449367831},
  lccn={2013454901},
  url={https://books.google.co.uk/books?id=a\_yXngEACAAJ},
  year={2013},
  publisher={O'Reilly Media, Incorporated}
}

@website{pickle,
title={Pickle - Python object serialization},
url={https://docs.python.org/3/library/pickle.html},
}

@website{sqrt,
title={Origin of Quake3's Fast InvSqrt()},
url={https://www.beyond3d.com/content/articles/8/}
}

@book{Lomont:2003,
  author          = {Chris Lomont},
  title           = {Fast Inverse Square Root},
  publisher       = {Purdue University},
  year            = {2003}
}

@InProceedings{ Rocklin:2015:scipy,
  author    = { Matthew Rocklin },
  title     = { Dask: Parallel Computation with Blocked algorithms and Task Scheduling },
  booktitle = { Proceedings of the 14th Python in Science Conference },
  pages     = { 130 - 136 },
  year      = { 2015 },
  editor    = { Kathryn Huff and James Bergstra }
}

@website{ssd_benchmark,
title={Apple SM0512G PCIe 500GB SSD Benchmarking},
url={https://ssd.userbenchmark.com/SpeedTest/25611/APPLE-SSD-SM0512G}
}

@article{Greengard:1987:JCP,
title = "A fast algorithm for particle simulations",
journal = "Journal of Computational Physics",
volume = "73",
number = "2",
pages = "325 - 348",
year = "1987",
issn = "0021-9991",
doi = "https://doi.org/10.1016/0021-9991(87)90140-9",
url = "http://www.sciencedirect.com/science/article/pii/0021999187901409",
author = "L Greengard and V Rokhlin",
abstract = "An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles whose interactions are Coulombic or gravitational in nature. For a system of N particles, an amount of work of the order O(N2) has traditionally been required to evaluate all pairwise interactions, unless some approximation or truncation method is used. The algorithm of the present paper requires an amount of work proportional to N to evaluate all interactions to within roundoff error, making it considerably more practical for large-scale problems encountered in plasma physics, fluid dynamics, molecular dynamics, and celestial mechanics."
}

@article{Epton:1995:SIAM,
  title={Multipole translation theory for the three-dimensional Laplace and Helmholtz equations},
  author={Epton, Michael A and Dembart, Benjamin},
  journal={SIAM Journal on Scientific Computing},
  volume={16},
  number={4},
  pages={865--897},
  year={1995},
  publisher={SIAM}
}